EM refactoring / EMv2 #193
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added 30 commits
August 15, 2023 16:34
…nd base class definitions from the base_class_templates nexus_definitions branch
…n already existent NeXus/HDF5 file
…t file based on an existent input-file to which then the template data are appended. This functionality is useful in cases when a scientific software has already generated a NeXus file but just some additional pieces of information are missing for the injection into the RDM. Examples of such missing info could be users, samples, project information, etc. This proof-of-concept implementation copies that input file and subsequently opens it as the output file and appends the template data subsequently. The current implementation does not verify though the NeXus content of this inputfile. However, in the future, this could be useful. The question is when to verify this and how: right after the copy?, after the template data were written?, or via loading all input file content first into the template and verify it as usual prior to writing to disk? While the latter idea enables overwriting content from inputfiles, the disadvantage is that template data might become too costly (wrt to memory demands, irrespective whether on the client or server side).
…s from phase_names based on a table composed from an EM domain expert
…airmat is not for some reason completely bypassed, some silent assumptions in nexus and the verification code?
…family files, bugfixing
…ut the calibration of ipf and roi axis coordinates uses pixels currently but should use pixel times scan unit, next steps: i) implement this and tree-based downsampling, ii) linting, styling
…this completes the implementation of the tech partner HDF5 parsers for EBSD, next step linting and adding EDS reader (for IKZ, etc)
…and ran successfully on all datasets, 3/13 contained relevant content
…de implemented but ROI code does not populate template, implement IPF computation
…ext to complete use case 3D EBSD
…ass xmaps, and H5Web refactoring done and working, 3D IPF maps is the only thing remaining for the DREAM3D example to work on the set of 3D example data
…l a bug with the zeroth dimension of the results array, IPF color map key renders correctly though
…IRmat user/project meeting but preparing the removal of the crystal xmap also for the 2D cases
…n base_class_templates branch
…o prepare with the resolving of possible merge conflicts
…hared VInP_108_L2 (IKZ Brückner, Bergmann), GeSi (IKZ Kernke), InP (PDI, laehnemann)
… xray line identification
…pdi/InGe, ikz/AlGaO, and ikz/GeSi example with EBSD maps also working
…plementation of Velox EMD parser v2
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Before this PR can be merged, #204 has to be merged, ruff applied, checks done, and respective nexus_definitions PRs merged into fairmat so that the em_refactoring can then use the correct version of the nexus definitions. |
mkuehbach
requested review from
sanbrock,
domna,
sherjeelshabih,
RonHildebrandt and
lukaspie
…imgs, adf, and ceta imaging modes. NeXus files were generated successfully but weird h5web display error coming up within ipynb, removechild tested if spaces in filenames cause this but no, in hdfviewer file shows without any issues
…rom FHI C. Rohner's example is parsed successfully, next steps: i) add Velox metadata schema version, ii) add microscope metadata, iii) merge PRs
…ctoring feature branch
sanbrock
requested changes
Feb 1, 2024
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- Rebase is needed as nyaml2nxdl has already been taken away.
- Restructuring is needed to move all debug/development code below the relevant reader subdir.
- Also note that quite some shared code exists which shall not be duplicated in specific readers, but rather could be collected in a generic util subdir.
- Note that different reader examples could be grouped and/or harmonised (and then documented) so users can chose which solution they want to follow.
- Documentation according to the new doc style needs to be added.
I would also like to add:
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@mkuehbach Area D is updating ASE to 3.22.1. Please have a look at this related PR as well: #263 |
sherjeelshabih
requested changes
Mar 13, 2024
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Closed as all development has been migrated to pynxtools-em, remaining suggestions from @sherjeelshabih have been resolved in that repo |
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The PR contributing the new em that includes all consolidated readers for em, including EBSD, spectroscopy/EDS/EDXS, nionswift, and plain images
This is a breaking change as em_om, em_spctrscpy, em_nion are about to become obsolete with this PR.
This PR on purpose does not include changes on atom probe tomography as this will be a new separate PR,
appdefs and base classes merged in by the base_class_templates PR #51 from nexus_definitions did not change APM-related classes